The size of the box is set on the conform page, find the following:
It is originally set to:
$Shipping_PackageArray[$Shipping_PackageIndex]["PackageType"] = "Flat Rate Box";
you can change that to:
$Shipping_PackageArray[$Shipping_PackageIndex]["PackageType"] = "Sm Flat Rate Box";
The valid options are:
Flat Rate Envelope,
Sm Flat Rate Box
Md Flat Rate Box
Lg Flat Rate Box